Molecular, kinetic, thermodynamic, and structural analyses of Mycobacterium tuberculosis hisD-encoded metal-dependent dimeric histidinol dehydrogenase (EC 1.1.1.23)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Quantum coherent tunneling between two atomic-molecular Bose-Einstein condensates

We study the quantum coherent tunneling dynamics of two weakly coupled atomic-molecular Bose-Einstein condensates (AMBEC). A weak link is supposed to be provided by a double-well trap. The regions of parameters where the macroscopic quantum localization of the relative atomic population occurs are revealed. The different dynamical regimes are found depending on the value of nonlinearity, namely, coupled oscillations of population imbalance of atomic and molecular condensate, including irregular oscillations regions, and macroscopic quantum self trapping regimes. Quantum means and quadrature variances are calculated for population of atomic and molecular condensates and the possibility of quadrature squeezing is shown via stochastic simulations within P-positive phase space representation method. Linear tunnel coupling between two AMBEC leads to correlations in quantum statistics.

Kinetic parameters for thermal decomposition of supramolecular polymers derived from flunixin-meglumine adducts

Meglumine, (2R,3R,4R,5S)-6-methylaminohexane-1,2,3,4,5-pentol, is a carbohydrate derived from sorbitol in which the hydroxyl group in position one is replaced by a methylamine group. It forms binary adducts with substances having carboxyl groups, which have in common the presence of hydrogen bonding as the main force in the stabilization of these species. During melting, adducts of meglumine with flunixin (2-[[2-methyl-3-(trifluoromethyl)phenyl]amino]pyridine-3-carboxylic acid) polymerize or self-assemble in amorphous supramolecular structures with molecular weights around 2.0 x 10(5) kDa. DSC curves, in a first heating, show isomorphic transitions where the last one at 137 A degrees C for the flunixin-meglumine adduct originated the supramolecular amorphous polymers with glass transition around 49.5 A degrees C. The kinetic parameters for the thermal decomposition step of the polymers were determined by the Capela-Ribeiro non-linear isoconversional method. From data for the TG curves in nitrogen atmosphere and heating rates of 5, 10, 15, and 20 A degrees C min(-1), the E (alpha) and B (alpha) terms could be determined and, consequently, the pre-exponential factor, A(alpha), as well as the kinetic model, g(alpha).

Kinetic parameters for thermal decomposition of microcrystalline, vegetal, and bacterial cellulose

Cellulose can be obtained from innumerable sources such as cotton, trees, sugar cane bagasse, wood, bacteria, and others. The bacterial cellulose (BC) produced by the Gram-negative acetic-acid bacterium Acetobacter xylinum has several unique properties. This BC is produced as highly hydrated membranes free of lignin and hemicelluloses and has a higher molecular weight and higher crystallinity. Here, the thermal behavior of BC, was compared with those of microcrystalline (MMC) and vegetal cellulose (VC). The kinetic parameters for the thermal decomposition step of the celluloses were determined by the Capela-Ribeiro non-linear isoconversional method. From data for the TG curves in nitrogen atmosphere and at heating rates of 5, 10, and 20 A degrees C/min, the E(alpha) and B(alpha) terms could be determined and consequently the pre-exponential factor A(alpha) as well as the kinetic model g(alpha). The pyrolysis of celluloses followed kinetic model g(alpha) = [-ln(1 - alpha)](1.63) on average, characteristic for Avrami-Erofeev with only small differences in activation energy. The fractional value of n may be related to diffusion-controlled growth, or may arise from the distributions of sizes or shapes of the reactant particles.

Molecular dynamics simulations on devitrification: the PbF2 case

In this work molecular dynamics simulations were performed to reproduce the kinetic and thermodynamic transformations occurring during melt crystallization, vitrification, and glass crystallization (devitrification) of PbF2. Two potential parameters were analyzed in order to access the possibility of modeling these properties. These interionic potentials are models developed to describe specific characteristic of PbF2, and thermodynamic properties were well reproduced by one of them, while the other proved well adapted to simulate the crystalline structure of this fluoride. By a modeled nonisothermal heat treatment of the glass, it was shown that the devitrification of a cubic structure in which the Pb-Pb distances are in good agreement with theory and experiment. (C) 2002 American Institute of Physics.

Kinetic parameters of polymer degradation by SAPO-37

High density poly(ethylene) has been submitted to thermal degradation alone, and in the presence of silicoaluminophosphate SAPO-37. The processes were carried out in a reactor connected on line to a gas chromatograph/mass spectrometer in order to analyze the evolved products. Polymer degradation was also evaluated by thermogravimetry, from room temperature until 800 degreesC, under nitrogen dynamic atmosphere, with multiple heating rates. From TG curves, the activation energy related to degradation process was calculated using the Flynn and Wall multiple heating rate kinetic model for pure polymer (PE) and for polymer in the presence of catalyst (PE/S37). SAPO-37 showed good selectivity for low molecular mass hydrocarbons in PE catalytic degradation.

Glutathione transferase pi (GSTpi) expression in breast cancer: An immunohistochemical and molecular study

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Combining genetic algorithm and simulated annealing: A molecular geometry optimization study

We introduce a new hybrid approach to determine the ground state geometry of molecular systems. Firstly, we compared the ability of genetic algorithm (GA) and simulated annealing (SA) to find the lowest energy geometry of silicon clusters with six and 10 atoms. This comparison showed that GA exhibits fast initial convergence, but its performance deteriorates as it approaches the desired global extreme. Interestingly, SA showed a complementary convergence pattern, in addition to high accuracy. Our new procedure combines selected features from GA and SA to achieve weak dependence on initial parameters, parallel search strategy, fast convergence and high accuracy. This hybrid algorithm outperforms GA and SA by one order of magnitude for small silicon clusters (Si6 and Si10). Next, we applied the hybrid method to study the geometry of a 20-atom silicon cluster. It was able to find an original geometry, apparently lower in energy than those previously described in literature. In principle, our procedure can be applied successfully to any molecular system. © 1998 Elsevier Science B.V.

Reinforcing and expanding the predictions of the disturbance vicariance hypothesis in Amazonian harlequin frogs: A molecular phylogenetic and climate envelope modelling approach

The disturbance vicariance hypothesis (DV) has been proposed to explain speciation in Amazonia, especially its edge regions, e. g. in eastern Guiana Shield harlequin frogs (Atelopus) which are suggested to have derived from a cool-adapted Andean ancestor. In concordance with DV predictions we studied that (i) these amphibians display a natural distribution gap in central Amazonia; (ii) east of this gap they constitute a monophyletic lineage which is nested within a pre-Andean/western clade; (iii) climate envelopes of Atelopus west and east of the distribution gap show some macroclimatic divergence due to a regional climate envelope shift; (iv) geographic distributions of climate envelopes of western and eastern Atelopus range into central Amazonia but with limited spatial overlap. We tested if presence and apparent absence data points of Atelopus were homogenously distributed with Ripley's K function. A molecular phylogeny (mitochondrial 16S rRNA gene) was reconstructed using Maximum Likelihood and Bayesian Inference to study if Guianan Atelopus constitute a clade nested within a larger genus phylogeny. We focused on climate envelope divergence and geographic distribution by computing climatic envelope models with MaxEnt based on macroscale bioclimatic parameters and testing them by using Schoener's index and modified Hellinger distance. We corroborated existing DV predictions and, for the first time, formulated new DV predictions aiming on species' climate envelope change. Our results suggest that cool-adapted Andean Atelopus ancestors had dispersed into the Amazon basin and further onto the eastern Guiana Shield where, under warm conditions, they were forced to change climate envelopes. © 2010 The Author(s).

The use of molecular spectra simulation for diagnostics of reactive flows

The C 2 * radical is used as a system probe tool to the reactive flow diagnostic, and it was chosen due to its large occurrence in plasma and combustion in aeronautics and aerospace applications. The rotational temperatures of C 2 * species were determined by the comparison between experimental and theoretical data. The simulation code was developed by the authors, using C++ language and the object oriented paradigm, and it includes a set of new tools that increase the efficacy of the C 2 * probe to determine the rotational temperature of the system. A brute force approach for the determination of spectral parameters was adopted in this version of the computer code. The statistical parameter c 2 was used as an objective criterion to determine the better match of experimental and synthesized spectra. The results showed that the program works even with low-quality experimental data, typically collected from in situ airborne compact apparatus. The technique was applied to flames of a Bunsen burner, and the rotational temperature of ca. 2100 K was calculated.

Identification of microsatellites markers associated with yield components and quality parameters in sugarcane

Marker assisted selection depends on the identification of tightly linked association between marker and the trait of interest. In the present work, functional (EST-SSRs) and genomic (gSSRs) microsatellite markers were used to detect putative QTLs for sugarcane yield components (stalk number, diameter and height) and as well as for quality parameters (Brix, Pol and fibre) in plant cane. The mapping population (200 individuals) was derived from a bi-parental cross (IACSP95-3018 x IACSP93-3046) from the IAC Sugarcane Breeding Program. As the map is under construction, single marker trait association analysis based on the likelihood ratio test was undertaken to detect the QTLs. Of the 215 single dose markers evaluated (1:1 and 3:1), 90 (42%) were associated with putative QTLs involving 43 microsatellite primers (18 gSSRs and 25 EST-SSRs). For the yield components, 41 marker/trait associations were found: 20 for height, 6 for diameter and 15 for stalk number. An EST-SSRs marker with homology to non-phototropic hypocotyls 4 (NPH4) protein was associated with a putative QTL with positive effect for diameter as also with a negative effect for stalk number. In relation to the quality parameters, 18 marker trait associations were found for Brix, 19 for Pol, and 12 for fibre. For fibre, 58% of the QTLs detected showed a negative effect on this trait. Some makers associated with QTLs with a negative effect for fibre showed a positive effect for Pol, reflecting the negative correlation generally observed between these traits.

Comparison of random regression models to estimate genetic parameters for milk production in Guzerat (Bos indicus) cows

Random regression models have been widely used to estimate genetic parameters that influence milk production in Bos taurus breeds, and more recently in B. indicus breeds. With the aim of finding appropriate random regression model to analyze milk yield, different parametric functions were compared, applied to 20,524 test-day milk yield records of 2816 first-lactation Guzerat (B. indicus) cows in Brazilian herds. The records were analyzed by random regression models whose random effects were additive genetic, permanent environmental and residual, and whose fixed effects were contemporary group, the covariable cow age at calving (linear and quadratic effects), and the herd lactation curve. The additive genetic and permanent environmental effects were modeled by the Wilmink function, a modified Wilmink function (with the second term divided by 100), a function that combined third-order Legendre polynomials with the last term of the Wilmink function, and the Ali and Schaeffer function. The residual variances were modeled by means of 1, 4, 6, or 10 heterogeneous classes, with the exception of the last term of the Wilmink function, for which there were 1, from 0.20 to 0.33. Genetic correlations between adjacent records were high values (0.83-0.99), but they declined when the interval between the test-day records increased, and were negative between the first and last records. The model employing the Ali and Schaeffer function with six residual variance classes was the most suitable for fitting the data. © FUNPEC-RP.

Kinetic parameters for thermal decomposition of supramolecular polymers derived from diclofenac-meglumine supramolecular adducts

Meglumine is an aminocarbohydrate able to form supramolecular adducts with organic acids. The recognition is based on hydrogen bonds and the structures resulting from the complexation have high solubility in water. This property has been exploited by the pharmaceutical industry in the improvement of existing drugs, and the successful example of this approach involves the poorly soluble non-steroidal anti-inflammatory drugs (NSAIDs). Investigation of the thermal behavior of adduct obtained from meglumine and the NSAID diclofenac revealed that a polymer-like material is formed from the self-assembly of diclofenac-meglumine adducts in the melt. This polymer showed a high molecular weight around 2.0×105kDa. The kinetic parameters for the thermal decomposition step of the polymer were determined by the Capela-Ribeiro non-linear isoconversional method. From data for the TG curves in nitrogen atmosphere and heating rates of 5, 10, 15 and 20°Cmin-1, the Eα and Bα terms could be determined, and consequently the pre-exponential factor, Aα, as well as the kinetic model, g(α). © 2012 Elsevier B.V.

Elucidation of carbohydrate molecular interaction mechanism of recombinant and native ArtinM

The quartz crystal microbalance (QCM) technique has been applied for monitoring the biorecognition of ArtinM lectins at low horseradish peroxidase glycoprotein (HRP) concentrations, using a simple kinetic model based on Langmuir isotherm in previous work.18 The latter approach was consistent with the data at dilute conditions but it fails to explain the small differences existing in the jArtinM and rArtinM due to ligand binding concentration limit. Here we extend this analysis to differentiate sugar-binding event of recombinant (rArtinM) and native (jArtinM) ArtinM lectins beyond dilute conditions. Equivalently, functionalized quartz crystal microbalance with dissipation monitoring (QCM-D) was used as real-time label-free technique but structural-dependent kinetic features of the interaction were detailed by using combined analysis of mass and dissipation factor variation. The stated kinetic model not only was able to predict the diluted conditions but also allowed to differentiate ArtinM avidities. For instance, it was found that rArtinM avidity is higher than jArtinM avidity whereas their conformational flexibility is lower. Additionally, it was possible to monitor the hydration shell of the binding complex with ArtinM lectins under dynamic conditions. Such information is key in understanding and differentiating protein binding avidity, biological functionality, and kinetics. © 2013 American Chemical Society.

Relações filogenéticas e filogeografia molecular das espécies de peixes anuais do gênero Simpsonichthys (Cyprinodontiformes: Rivulidae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)